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- PDB-8cs8: [High G:C, High Vapor Diffusion] Self-Assembled 3D DNA Hexagonal ... -

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Basic information

Entry
Database: PDB / ID: 8cs8
Title[High G:C, High Vapor Diffusion] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle
Components
  • DNA (5'-D(*GP*AP*GP*GP*AP*GP*CP*CP*TP*GP*CP*GP*CP*GP*GP*AP*CP*AP*GP*AP*G)-3')
  • DNA (5'-D(*TP*CP*CP*TP*CP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*GP*CP*GP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*CP*C)-3')
KeywordsDNA / Tensegrity triangle / synthetic construct / self-assembly
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å
AuthorsLu, B. / Vecchioni, S. / Ohayon, Y.P. / Seeman, N.C. / Mao, C. / Sha, R.
Funding support United States, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CTS1120890 United States
National Science Foundation (NSF, United States)CCF-1117210 United States
National Science Foundation (NSF, United States)EFRI-1332411 United States
National Science Foundation (NSF, United States)CHE-1708776 United States
Office of Naval Research (ONR)N000141110729 United States
Office of Naval Research (ONR)N000140911118 United States
Department of Energy (DOE, United States)DESC0007991 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles.
Authors: Lu, B. / Woloszyn, K. / Ohayon, Y.P. / Yang, B. / Zhang, C. / Mao, C. / Seeman, N.C. / Vecchioni, S. / Sha, R.
History
DepositionMay 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Aug 16, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.pdb_format_compatible
Revision 1.4Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*GP*GP*AP*GP*CP*CP*TP*GP*CP*GP*CP*GP*GP*AP*CP*AP*GP*AP*G)-3')
B: DNA (5'-D(P*CP*CP*GP*CP*GP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*CP*C)-3')
D: DNA (5'-D(*TP*CP*CP*TP*CP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)12,8004
Polymers12,8004
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*GP*GP*AP*GP*CP*CP*TP*GP*CP*GP*CP*GP*GP*AP*CP*AP*GP*AP*G)-3')
B: DNA (5'-D(P*CP*CP*GP*CP*GP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*CP*C)-3')
D: DNA (5'-D(*TP*CP*CP*TP*CP*TP*GP*T)-3')

A: DNA (5'-D(*GP*AP*GP*GP*AP*GP*CP*CP*TP*GP*CP*GP*CP*GP*GP*AP*CP*AP*GP*AP*G)-3')
B: DNA (5'-D(P*CP*CP*GP*CP*GP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*CP*C)-3')
D: DNA (5'-D(*TP*CP*CP*TP*CP*TP*GP*T)-3')

A: DNA (5'-D(*GP*AP*GP*GP*AP*GP*CP*CP*TP*GP*CP*GP*CP*GP*GP*AP*CP*AP*GP*AP*G)-3')
B: DNA (5'-D(P*CP*CP*GP*CP*GP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*CP*C)-3')
D: DNA (5'-D(*TP*CP*CP*TP*CP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)38,40112
Polymers38,40112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)126.928, 126.928, 57.857
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*GP*AP*GP*CP*CP*TP*GP*CP*GP*CP*GP*GP*AP*CP*AP*GP*AP*G)-3')


Mass: 6563.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*GP*CP*GP*CP*A)-3')


Mass: 2083.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*CP*TP*CP*C)-3')


Mass: 1785.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*CP*TP*CP*TP*GP*T)-3')


Mass: 2368.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 10.51 Å3/Da / Density % sol: 88.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 800 mM Tris, 800 mM Acetic Acid, 20 mM EDTA / Temp details: 338-293 at 0.4/hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00743 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 6→64.96 Å / Num. obs: 1146 / % possible obs: 86.4 % / Redundancy: 19.6 % / Biso Wilson estimate: 342.07 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.8
Reflection shellResolution: 6→6.85 Å / Num. unique obs: 192 / CC1/2: 0.677

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R96

7r96


Resolution: 6→54.96 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 39.1215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3015 71 6.26 %
Rwork0.2313 1063 -
obs0.2364 1134 80.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 578.42 Å2
Refinement stepCycle: LAST / Resolution: 6→54.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057956
X-RAY DIFFRACTIONf_angle_d1.76821467
X-RAY DIFFRACTIONf_chiral_restr0.0613166
X-RAY DIFFRACTIONf_plane_restr0.004642
X-RAY DIFFRACTIONf_dihedral_angle_d38.0762406
LS refinement shellResolution: 6→54.96 Å
RfactorNum. reflection% reflection
Rfree0.3015 71 -
Rwork0.2313 1063 -
obs--80.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.645656220375.170411179886.106283813227.34524754196.398689535562.5399465309-0.3494583510222.66137908789-3.240946759783.621295890722.684145953930.8261894620982.118273270382.42043767866-0.2522268664056.31726133564-0.7120404361350.3794119747314.89621734797-2.423479506716.67004705372-48.325537413930.196577178416.0456296023
22.30591649780.8495527301711.695258343242.51197358959-1.729318457313.82720533884-1.891091490332.748098235150.835339261513-1.41026004934-0.496952007302-6.577801965552.337801030482.346537236951.815017909154.927567977161.36650138119-0.3280076691014.40866183594-2.144367171519.79206649789-51.305739826729.186507582514.620480568
33.191169934122.962849852771.289777856553.949031653330.04195334493762.351617204461.72110895817-2.00495435874-3.568110691312.563212225920.6414780090692.812157163860.163295279525-2.67045964319-2.003728268583.558539407140.5362239098470.7879656061965.10911751172-1.076356029257.88321666773-38.71938745941.832273783926.8804929407
40.914378414554-0.5387352132670.9306691224440.633087256330.7053946702983.974446325050.4156331543030.2815657112741.58453388454-6.096966088950.09795882587960.4842714665463.398362072510.374003130515-3.229191752527.901571022061.581722234210.3121441887383.1211414704-6.890297228327.12917376035-61.888199132811.97199763712.29101809164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 101 through 121)AA101 - 121
2X-RAY DIFFRACTION2(chain 'B' and resid 119 through 125)BB119 - 125
3X-RAY DIFFRACTION3(chain 'C' and resid 209 through 214)CC209 - 214
4X-RAY DIFFRACTION4(chain 'D' and resid 201 through 208)DD201 - 208

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